I feel Mario may have a very slight advantage against Greninja. We have to play rather differently against Mario than some other characters, with lots of Fairs, Utilts, and Fsmashes. For as much as Mario has in the way of combos and kill power, he doesn't have very good range. It should also be noted that his Dthrow to Utilt (or even jab) doesn't seem to work as well against Greninja due to our low landing box (it can still work starting at around 20%, but that gives him at most about a 20-30% combo which is pretty good compared to most characters). Now, considering the cape, we do have to play intelligently with Shurikens. This is one MU I don't think we should ever use a fully charged Water Shuriken in except in the most situational positions (i.e. when he's recovering and lacks a double jump and cape boost). However, the smaller charged shurikens are generally good to disrupt him.
If he approaches with Fireballs, I feel it's best if we either A. shield and pursue him to punish their ending lag or B. jump over the Fire Ball and Bair. The Fireballs come at that dreaded 45 degree angle, so it is kind of a pain to get around them, though. We also need to be very cautious of his Dair. It starts killing at around 170% iIrc, and it's very easy to get hit by it due to our lack of disjoints. I'd advise trying to get out of its maximum range (maximum range being how much range Mario can cover with it if he keeps going toward Greninja in the air with it) and trying to ward him off with Fsmash (or if you can, baiting him into going all the way with it and punishing him with said Fsmash).
Now, as with many of Greninja's MUs, it's pretty tough getting a kill on Mario. At the same time, Mario himself has very few reliable kill moves, and thankfully for us, ours tend to outrange his. I feel our best kill moves in the MU are Fair and Fsmash, with special mention to Bair if you can read his recovery (which isn't too hard given we're talking about Mario). Just be wary of his Fsmash, Dsmash (which now hits harder on the back hit I believe), his grab at very high percents, and his Usmash, especially when landing. Thankfully, due to Greninja having a tendency to duck when you land, I believe you can safely airdodge any Usmash attempts.
Now, for the hard part. Alright, Mario got a kill on your or has a huge advantage against you, and he refuses to approach. This is where the MU becomes fairly irritating. You need to weave through the fireballs and find some way to punish him with, well, anything. Don't just SH Nair, though. He will shield it and then proceed to grab or OoS Nair. Fair is also quite a bit of a commitment for trying to approach, though, and Bair lacks a disjoint. I feel that our best approach is honestly jab to catch him coming back down from the air. Just empty short hops into jabs and Dtilts for poking. Again, though, approaching Mario as Greninja is fairly difficult, so try to stay ahead in the match as much as possible to force the opposite situation.
Now, let's get into customs. Fast Fireball only accentuates the problems that Greninja has against Mario. Although the Fireballs each do only about 1%, Mario doesn't need to jump at all to cover an insane amount of distance. Gust Cape also neuters our approaching game somewhat. Thus, what was once at least slightly manageable becomes as annoying and ordeal as trying to get in against Toon Link. We can't crawl under the Fireballs, either. Basically, your best bet, in my opinion, is to approach via the air and trying to limit Mario's space. Like with Mega Man's jab, we are able to jump over Fast Fireballs and Fair for the punish. If Mario tries to escape, just chase him down. Otherwise, be very aware of his options and try countering accordingly.
Thankfully, if we do get the first KO, Mario is forced to approach, and while the Fast Fireballs do help him in that regard as well, like with Vanilla Mario, we can carefully space out Fairs and Fsmashes to tack on percent before he KOs us. Remember to not panic if he hits you with a Fast Fireball in the air where he's in a position to fall and immediately Fsmash or Dsmash. Just fast fall and shield to avoid the Smash (as long as you're close enough to the ground, otherwise, DJ or Hydro Pump away). Also be even more so aware of approaching with Nair if he has Explosion Punch. It gives him yet another OoS option against even spaced Nairs. Finally, High Pressure F.L.U.D.D. is a blast to the past as it can gimp us much the same way we used to gimp others. If he has this, make sure to always recovery low. Greninja has the air mobility to generally get us right under the ledge before we have to Hydro Pump, but make sure to mix it up with diagonal Hydro Pumps toward the ledge as well as Mario is able to Bair us and stage spike us if he catches on to that recovery.
Overall, while Mario does have trouble killing us, he does have quite a few tools to mess up Greninja. It's not an unwinnable MU by any stretch. We do, for the most part, outspace him, but his projectile game is pretty good at tacking on a lot of percent by itself, and his ability to force us out in CQC along with the ability to somewhat mitigate our Shuriken game definitely hampers our ability to put pressure on him.
While I have played a couple of Luigis, I don't really have too solid a grip on the MU. I would say that it is slightly in Greninja's favor, though. Without the cape and the Fire Balls going horizontally at a much slower rate than Fast Fireball, he kind of loses the advantages Mario had in the MU in exchange for slightly safer kill options. Like with Mario, we can potentially gimp him as well (or tack on a lot of percent trying).
Dr. Mario is a complete mystery to me, but I'd imagine he'd be easier than both Luigi and Mario due to his horrid recovery.