IMO:

It would be a stretch for you to get accepted directly into Masters program.  3 year Bachelors degrees from Nepal normally do not get recognized in the US.  Assuming you did very well in GRE and GRE Subject (Chemistry in your case) test and have several years of solid academic research experience in your field - you already mentioned you have good grades, hopefully that will translate to 4.0 gpa or very near - you could write a strong statement (application essay) to argue that you are ready for the rigors of grad work to stand a chance.

It is probably best if you do your Masters in Nepal and apply for PhD program here in the US afterwards.

Again, IMO.