Up Your Arsenal would definitely be my number one choice for best Ratchet and Clank game. It was the first Ratchet game that I ever bought and I've enjoyed every single moment of it, especially when both single and multiplayer modes were pretty solid and fun in this game.
Runner up would either have to go to A Crack in Time or Tools of Destruction. It's hard to pick which.
A Crack in Time was great for it's new innovations, gameplay and amazing animations in the cutscenes. Tools of Destruction was great with it's charming humor, great story and fun, but usual gameplay that's like in the PS2 Ratchet and Clank games, but with next generation visuals.