I am finished with both Genki books and my teacher wants me to buy a more intermediate book however I'm unsure between Tobira or Minna ni Nihongo 2. Any ideas?

Careful if you buy online, what you want is called Minna no nihongo (MNN) 中級 (chuukyuu), which is composed of two courses MNN 1 and MNN 2, just like MNN　初級 (shokyuu) had also two sets of books also called MNN 1 and MNN 2.

As for the comparison between Tobira, I don't really know, but I know MNN 中級 is like MNN 初級 which means kind of boring and systematic. If you hear Tobira is less boring you should go for it.

I've heard relatively decent things about Tobira, and I know my Japanese class is going to start with Tobira next semester, if that helps you at all

I like Tobira because it doesn't use the standard business/school settings that most texts do. Each chapter focuses on a different aspect of Japanese culture, which makes going through the lessons more interesting.
Can't speak for Minna no Nihongo 2 though. Sorry!

The Amazon reviews for Tobira are positive and informative:

http://www.amazon.com/TOBIRA-MAYUMI-ET-A...4874244475

I'd cast a vote for tobira (I have both). The main text is very well put together with longer readings that gradually scale up in difficulty. It also includes a good mix of short conversations in various politeness levels. All text includes audio, which is nice. If you end up liking the main text, there is a supplementary grammar book as well as kanji book available as well.

I can't comment about Minna no Nihongo 2 but I'd also like to say that Tobira is pretty decent if you liked the Genki textbook series.