In my opinion you can determine a "best" and not just a "favorite" in this category. The answer is EVH, and there really isn't a close second.
Think about everything that goes into being a great player - in no particular order of importance:
1. Great technician - No one in the history of the instrument has generated more sheer "wow" factor than EVH. From the first note, everyone recognized this guy was an explosion of talent.
2. Originality - The taps, the dive bombs, the licks, etc. One of, if not the most, original, distinctive players ever.
3. Equipment - Here's where EVH is number one by a huge, huge distance. From the development of the Floyd Rose down to the simple little D Tuna. He created the most famous guitar of all time: the original super strat.
4. Tone - The Brown Sound. Nuff said.
5. Stage presence - That goofy smile hid the fact that the dude is basically a dick. No one's ever looked cooler playing guitar.
6. Influence - Does anyone remember that for one year in the 80's (87?) KRAMER was the highest selling guitar brand? There's only one reason for that. Everybody was dive bombing and tapping on super strats to the point of nausea. When you think about it, EVH caused the '91 Grunge movement, because his influence over style and songwriting was so great, it caused a tipping point of over-saturation.
7. Songwriting - He was the lone real songwriter in the band. No need to list the songs because we all know them.
When you add up all the factors, its a surprisingly easy choice in my opinion. I've got other players that I enjoy more as "favorites", but there's only one objective best, and that's EVH. If he had died in 1989 we wouldn't even be having the conversation. It would be a universal given.