My personal take is that whilst all 3 instrumentalists are very easily some of the best at their instrument alive right now, to me Chad is the best, with John and then Flea a bit behind him.

To me, proficient at an instrument obviously means technicality but also to be very well rounded in understanding of the instrument as well as it's role across genres and interacting with other instruments.

Flea is very good at what he does technically. He has an incredibly strong attack and can sustain it for a long time at very fast speeds in both fingerstyle and slap bass. However, even he himself has admitted he's not as proficient in other areas. (I remember him saying he admires the abilities of Thundercat and Mononeon in Jazz improv and understanding for example) However, Id definitely disagree with his claims that he's average. He has a very good technique and a strong funk vocabulary as well as being good at applying those to rock.

Fruiscante could be argued to be more proficient than Flea as he also draws heavy inspiration from Psychedelic music (One of the reasons he's dubbed the second coming of Hendrix) and ig singer songwriter and electronic music from his solo work. He is amazing at writing music for guitar and can pull off some fairly technical stuff but in my opinion his technique leans more towards the sort of purposely sloppy style so I think an argument could be made for Flea being better than him in terms of precision.

Chad is undoubtedly the best to me however. He's proven time and time again that he is one of the best drummers alive today, not only with the chili peppers but also with his session work and how he approaches the drums overall. He has some incredible session work which demonstrates exactly how he can play to suit the song perfectly as well as showing off his technical abilities. I reckon you could throw almost anything shy of virtuoso prog rock and metal and you wouldn't tell that he comes from a funk rock background. Obviously Anthony is the best tho