I am 2 weeks late. I have taken two home pregnancy tests and they were both negative. I am having hot flashes, nausea and severe fatigue. I also have lower stomach pains/cramps. Since I don't have cramps I can't just pop into an OBGYN's office so I need to know if I even should be worrying or if I should wait?

Did you take any of the tests recently? If not, try another one making sure that you follow the directions carefully. Otherwise, you could see if there is a pregnancy center near you, health department or a planned parenthood to obtain free or low cost testing. You could also just wait and see what happens when your next period is due and test again at that time if still no period.
If you aren't comfortable waiting that long, and you don't believe there is a location near you to obtain testing, then you could just try a pregnancy test each week until you are due for the next period.

My period came today actually after a trip to the ER and there is nothing severely wrong, well anything reproductive wise at all which leads to a new question; why am I not getting pregnant?

How long have you been trying? Most couples will become pregnant within a year of trying, but it can take longer sometimes, even when everything is fine.