Applying to MSc vs PhD in CS with science background in US
I'm no expert, but with research experience and already having a Masters in physics, I think that you should directly apply to the PhD programs.  During your first two years, you're going to take courses anyway.  So unless you don't think that you'll be able to handle those courses, I think that doing another masters and then your PhD will be a waste of time and money.  It depends on where you want to go, but a lot of schools will make you take courses in your PhD even if you already have a masters in CS.