There is nothing sensitive about my work, so don't have that to worry about. Sciency stuff and completely open to the world. At this point I feel that even if I stayed it would not benefit either party.
I don't hate my boss which makes it harder. I am the only developer for this piece of the project and replacing me will take time, the schedule will slip and put her in a tough spot.
Do you know if I should tell my boss I see everyday that works for the government agency, or the one off-site for the contracting company I am hired through?
Then I'd personally say everyone's advice is pretty spot on, this isn't going to hurt you just do it and be up front. And tell them both, order in my opinion would be the company you are hired through first and then the agency. Just depends on your relationship with both parties, as I don't think you can go too wrong long as you tell them both timely.
Just remember, if a company doesn't want you there they will walk you out whenever they want, so it is a business transaction as someone else pointed out, but one that is somewhat lopsided generally in favor of the employer. So you are right to be cautious, but don't stress yourself to death, do it and be happy.
I don't hate my boss which makes it harder. I am the only developer for this piece of the project and replacing me will take time, the schedule will slip and put her in a tough spot.
Do you know if I should tell my boss I see everyday that works for the government agency, or the one off-site for the contracting company I am hired through?