As others have said, the phrases are synonymous since looks like is a figure of speech (I believe it would be more correct to say looks as if), and I would say both sound natural. It comes down to your choice of tone. Do you want a colloquial/vulgar sound? Is the person speaking calm or rushed? Is the person's presence in the lobby threatening?
These questions might lead you to select one of the following or even some other structure:
- Seems we have company (this one is better than 2 because have is less vulgar as seems is less vulgar)
- Seems we got company
- Looks like we have company
- Looks like we got company (this one is better than 3 because got is more vulgar as looks like is more vulgar)
- It seems we have company (more calm than 1)
- Looks as if we have company (more calm than 3)
- It looks as if we have company (more calm than 6)
I would avoid putting have and got together, though, since they're redundant. Further, that is one of the most overused words in colloquial English, today, at least in America. As soon as you say it or type it, you should ask if it's necessary and try to remove it.