Joe's tone has changed over the years as he's developed new pickups, amps, pedals, and so on...he's still always able to play pretty much everything, though, which should tell you that the majority of it is in his fingers.
Agreed. People who are new to guitar often fall into the trap of 'great tone', thinking they can buy it from guitar center. 90% of all tone of all players is in their fingers. The guitars, pedals, amps, strings, and setups and yada yada simply augment the innate tone that they carry with them wherever they go.
For example. Whether Eric Johnson is playing a gibson, or a fender, through a fender twin or a rectifier, it's STILL gonna sound like Eric in any combination of the above. That sweet, almost violin quality of his vibrato is gonna come through, because it's in his fingers. Same with Satch, Vai, and Malmsteen. Ok, well, Malmsteen was robbed of his unique tone by the countless legions of Yngwieinites who capitalized on his efforts and became arpeggiator robots. Most of them can be found on youtube these days sweeping away, all claiming to be the 'world record guitar speed' holder!
The finger's part in the 'tone' can't really be 'learned' in my opinion. It can, but it takes time and feeling in order to nail it. That's the cool thing about guitar though. There are so many subtleties that can come through in your playing once you've found an identity with your instrument, that it's literally possible for your guitar voice to be as unique as your fingerprint. Hell, your fingerprints probably have something to do with your tone at some microscopic subcutaneous level.
Of course, I'm not saying that equipment won't have a big impact on your tone. Absolutely it will! But again, it's more of an augmentation of what's already there in the relationship between your fingers and your strings. SRV's tone probably would not have been half as sweet if he wasn't playing those monster-thick cables on those old strats. In fact, his tone likely suffered in the form of detuning whenever he picked up a shred guitar with really light gauge strings.
My own music (myspace.com/sonicenergy) reflects what's between my fingers, the strings, and my wang bar (the one on my guitar). I'm no Joe, Vai, or Johnson, and will never be, but I have my own ID with the guitar, and I like to think it's unique. I didn't search it out or try to copy anyone to arrive at it, and in the process, I've found something that I can call my own. It's not as fast or precise as some of the really great players who log hours a day, but it's there nonetheless, and I have loads of fun with it!
The point is, foster the relationship between your fingers and the strings, and you'll find your tone. Then, you'll be able to express it through any guitar and a plethora of cool neo-gadgetry! If you can afford it, that is....