I don't know how other people would answer this one, but I personally consider a TARDIS "Team" to consist of the Doctor and at least two other companions. I'm not really sure we've had one of those in the new series other than the Doctor, Amy and Rory, so they get the title of "Favorite" (I'm sure someone's going to come in and slap me around for saying that, but they can do the meme themselves if they want to).
And I couldn't find a suitable video or picture of the Doctor, Amy and Rory that I wanted to post here, so have a video of Matt, Karen and Arthur singing Christmas carols. Because those three are just plain adorable and awesome and I love them:
(ETA: Okay, okay - Series 1 did have the Doctor, Rose and Captain Jack for three stories - even threw Mickey in the mix there for a bit. But I stand by my choice of the Doctor and la familia Pond).