Nearly every name will go with Thomas - it's so ubiquitous that most types of name will match it.
Since you've picked a formal name for your son (as opposed to naming him Tom or Tommy on his birth certificate), I think it makes sense to do the same for your daughter - but most of your names you've listed don't conform to that. By and large, you've just listed a lot of nicknames - which would work well if you had a 'just' Tom.
On that basis, I'd pick Eva, Olivia, Lily, Mia, and Summer from your list. I'd probably cross a few off them off it it were my own list for being too popular (in a way that Thomas isn't - Thomas is perenially popular; the girls' names you like have seen more peaks and troughs and are currently riding high). I think you need something a bit less 2012 and a bit more, 'Could have been born at any point in the last 100 years.'
With a name like Thomas, I'd be inclined to pick something equally classic (as I like names to match in styles). For me, that would mean considering names like Alice, Anna, Caroline, Catherine, Charlotte, Eleanor, Elizabeth, Emily, Emma, Leah, Lucy, Rachel, Rebecca, and Sarah. I'd probably add Molly - an 'established' nickname, much like Daisy - to that list too.