I'd say there are about equal. If Lee wins I think it's pretty likely that his will power will be his winning tool in the fight, don't you think? When you look at all of Neji's abilities and compare it to Lee's pure taijutsu move set, their minds will easily start shifting towards Neji but that's not always the case. Guy is known as Kakashi's rival, who has the Sharingan, is a natural prodigy/genius, and has loads of ninjutsu over him. Likewise, I really doubt Lee is going to beat Neji with less than high difficulty if he does.
On a side note.. poor Lee. His dream was to surpass Neji and show his work but did they ever show their fateful final battle? I'd rather have Neji stay dead but damn.