"Excuse me, where's our classroom?"
A little surprise for me too this sounds not very natural. Please stick to 在.
It is not wrong though and I would say it for some place I have never heard before and have no idea where on earth it is, e.g. 雷克雅未克是哪里？Where is Reykjavík?
For using 是, my question would be 我们的教室是哪一间？.
Another option is 我们的教室是在哪里的？.