History might swap this around a bit but Rift Apart is currently my favourite. I felt the gameplay was the most refined, the worlds were the prettiest, the story was the best, and I totally have a crush on Rivet. The side content was pruned a bit - which I prefer, because the core shooting gameplay loop is why I play Ratchet & Clank, not the puzzle solving.
Crack in Time is #2, followed by Up Your arsenal and Going Commando, then the 2016 Remake (Because it's basically the story of #1 with the gameplay of the most recent games). 2002 hasn't held up as well as the other games but I still love it.
My Console Library:
PS4, PS3, PS2, PS1, WiiU, Wii, GCN, N64 SNES, XBO, 360
3DS, DS, GBA, Vita, PSP, Android
Top 6 this generation:
Bloodborne, Sekiro: Shadows Die Twice, God of War, The Legend of Zelda: Breath of the Wild, Dark Souls III, Red Dead Redemption II, Rock Band 4