In a formal professional setting, it can be better not to discuss another person's appearance. Some people take compliments better than others and some will read more into it than you mean regardless of what you say.
Complimenting appearance is generally (arguably) more commonly done by women to other women or (less frequently) men. There are times where a male may compliment a female, particularly likely at a special event or out-of-work meeting where their dress is considerably different from their usual appearance. Note that this is a generalization and does not necessarily apply to all people.
If you feel it necessary, I think that the most gender non-specific way of telling someone they look good that won't have any issues with impropriety is to say:
You look nice.
This can seem a bit vague but it can still be very effective if you make it specific to the person you're addressing and how you say it will make it seem sincere.
You can add a bit to it to make it less terse,
You look very nice tonight.
It can also be followed by a specific thing you think they've done well:
You look nice. I really like your dress/suit.
You look nice. That color really suits you.
You could also go this route but be careful to use only if it's really obvious they've made a change to their look:
You look nice. Did you get a new hair cut/glasses?
In general, people like getting affirmation that their new look suits them as they can be a little unsure.
This can all go out the window the second you become friendly with your coworkers/boss and your gender in relation to theirs can greatly affect what's appropriate.