I think they are both highly rated amongst those who like a multi doctor story. I've certainly havent gathered from here that there is some generally agreed thing that one was miles ahead of the other in terms of quality, and that there was some big problem with one or the other (apart from the odd few who believed that the 50th wasn't proper because Moffat couldn't magically de-age the actors of the 4th-6th doctors, and magically ressurect the first three actors, for them all to be in it (even though he still found a way to get them all in it in some form)).
For me, I prefer the 50th, but only because it is of my time, and I 'was there' so to speak, and yes, because the main focus is on Doctors of my time.
Also, don't forget, Tom Baker actually did the 50th

.
Despite not having watched any of the first 2 Doctors (except for part 1 of An Unearthly Child) and barely any of the 3rd Doctor, I found the five Doctors to be a good bit of fun, with an entertaining enough story, and enjoyable to see the incarnations to interact.
My only real problem with both the 5 and the 3 doctors, is that they have the 2nd and 3rd doctors squabble as if they are different men, and that the 3rd doesn't even particularly remember being the 2nd.
The one I think is underated is The Two Doctors. I find it fascinating to see a quieter, non special, multi doctor story, featuring two Doctor's whose era's were so far apart. I like how it's a story which finds a completely non forced way to involve the two, and isn't afraid to take risks with the format, such as starting the episode with a large chunk of the past doctor, before we even see the current doctor, something which I couldn't imagine in any other special.
I'd love to see an in series Two Doctors for today, just in series, no fanfare, normal plot, which accommodates the current Doctor and a past one. I think, written by the right person, they could make it so that it makes the current one really reflect on who he is, who has been in the past, and who he'd like to try and be in the future.