Hey guys, so I have a question about selecting my major; currently, I'm missing one course from the pre-reqs required to get in to Env.Sci/Geography; if I take the missing pre-req during the summer, can I still get in?

Yes, if it's offered during summer of course.

So when I apply to Level 2 Programs in March/April, should I still apply to the one I'm technically not eligible yet?

Yes, but they may not accept you - if you still want to get into the program, you can always switch into it at the beginning of 2nd year.

If your marks in the other subjects are fairly strong, you should be alright to get conditional acceptance

I was in that situation and was accepted conditional upon taking the course in the next available semester. So yes, apply anyway.