Top 5 teams in all of FRC history? That's a tough one...
71: Any top 5 list that leaves off the only 4-time World Champion is deserving of being the Rough Terrain--run over very often. They also have a World Finalist to their credit, and some RCAs as I recall. Oddly enough, only the Finalist came in the 3-team-alliance-on-the-field era.
254: HoF team, 1 World Championship, and on top of that has one of the most impressive streaks at a single event, with only one non-win at SVR dating back to 1999.
2056: They've won everything except the World Championship... except that one regional this year

. There are those that say they should have filled that hole in 2012.
1114: Not as dominant as 2056, but still a force to be reckoned with.
And the last spot goes to... TIE!
67: Dominant every year, and still the only team to pull off a World Championship and a CCA at the same time.
47: I never got to see this team in person, but they are LEGENDARY. Pioneers of swerve drive, powerhouse when 71 was on the rise... and if it wasn't for this HoF team, this website wouldn't exist. (Their legacy lives on in FRC0051, which is a combination of FRC0047 and FRC0065.)
And a couple of Honorable Mentions...
191 is the only team with a guaranteed 3 berths at Championship. One for being a Legacy team, and one for each of their TWO Championship Chairmans' Awards. They are the only team with more than one CCA. (And yes, they only use one of those berths.)
111 is another legendary team, with that unforgettable tie-dye and a history of "just complex enough for the job" robots--OK, so maybe a 7-DOF arm is a little overkill for most teams...