According to the Social Security Administration's statistics, last year, among boys and girls given the name of "Skyler", the boys were ahead by 13 percent.
On the other hand, among boys and girls given the alternate spelling of "Skylar", the girls led by 70 percent. So it would seem that "Skylar" is perceived to be the more feminine spelling of the two.
Personally, I like "Skylee", because if you have another girl you can name her "Kelsey", which is an anagram of Skylee. :)
-- Nanaea