No, Eden is not a boys name, unisex at most. According to my name dictionary (published back in 1983): 'In modern times male and female Edens seem to exist in almost equal numbers.' It also mentions that 'the 17th cen. Puritans probably began the fashion for using Biblical place names as first names, especially for women, perhaps because far more men are mentioned by name in the Bible than women.' So there probably have been more female Edens overall.
It does sound very feminine to me, maybe partly because the first time I came across it was for a female character in a book. It's a nice sound, not harsh at all, with lovely associations of course.
I quite like Ellen, but somehow it has a slightly drab vibe, compared to Helen/Helena or Eleanor.