Having a period is not a guarantee that you are not pregnant, just like not getting your period is not a guarantee that you are. Some women have late periods for reasons other than pregnancy, and some women do bleed in early pregnancy. Our bodies all react to things a little differently, so you never know.
There's a good chance you're not pregnant, but you could take a test if you want to make sure. Taking a test is the only way to know for sure.
If you told your boyfriend "no," and he put his penis in you anyway, that is rape.