"Tomboy" but in reverse
Language Locks
The key problem with finding such a word is that our entire culture and language is set up to view masculine traits positively and feminine traits negatively. It’s just as built-in as thinking of left being something sinister (like a left-handed compliment) and right as something that is good and proper (like righteousness and human rights).
Don’t believe me that it’s hardwired into our entire language? Countless examples exist. One cannot speak of being virtuous or having virtues, let alone of virility, without ultimately tracing back to vir, the Latin word for a man.
Another would be the way that the majority of English poetry employs something that has come to be called masculine rhyme, with a final strong syllable rhyming at the end — in opposition to feminine rhyme, where the final syllable or syllables are unstressed: weak.
So while it is seen as socially acceptable, indeed at time even even desirable, to ascribe to a woman various stereotypically masculine traits in a positive way that makes us view her positively, it is exceedingly difficult to ascribe to a man any stereotypically feminine trait in a way that does not seem to put him down.
It’s exceedingly difficult to break out of this lock on language, culture, and connotation. Even the original poster’s tomboy is a compound word formed of two words that both mean something male — a tom and a boy — yet we now use them together on a female without denigrating her. It doesn’t work the other way around. If the opposite of boy is girl and the opposite of Tom is — well, just pick any girl’s name you please, like perhaps Nell — you’ll find that calling a lad a nellygirl is certain to be taken as an insult.
The locks aren’t just on language, either. It’s on hair, too. Notice how a short-haired woman is considered butch, while a man with long locks is often considered if not exactly effeminate, at least part of the counterculture not the professional one.
Enter the metrosexual
Existing words like androgynous or epicene don’t really work, because they partake too much of an undecided, decadent, or even sybaritic nature, all of which are considered undesirable.
We do have one neologism of recent coinage, though, that takes a stab at doing just this very thing: that word is metrosexual.
It was invented mostly for marketing purposes, so I’m far from completely certain of the word’s real success in creating such a word with positive affect, nor of its ultimate fate as a word that endures outside the muddled mumblespeak of marketeers’ prattle. But it does now exist, at least for a while.
I do wish there were something better than this; see my initial comment to the OP’s question. Good luck on your quest.
The best word that I could image in the word "effeminate." Merriam-Webster defines it as "having feminine qualities untypical of a man" which seems to have exactly the connotation you are referring to. This term is rather derogatory, however, so it may not be perfectly comparable to the term "tomboy." The other definition for effeminate shows the gender bias, this time in the opposite direction, at work. Merriam-Webster also describes effeminate as "marked by an unbecoming delicacy or over-refinement."