Should I inform students that there are cheaper alternatives to the on-campus book store?
Politically? 

Sure, but there is always a chance that you will step on someone's toes if you do anything. I fully agree with Nicholas that you have subtle ways to do it.

Ethically?  

In the given situation the bookstore is a for-profit entity that gives below-average service to your students on an above-average price. Whatever approach you use to define the main mission of a university, it should include a good and fair service to your students for their 10-20-30 k$/year they pay. So I would say it is unethical to not tell them that they are not obligated to use a sub-par money-sucker service, and they are free to buy from internet, e.g. Amazon. If anyone is unethical in this situation, it is the person who is supervising the B&amp;N shop's license to run at your university. But it is again a politically sensitive issue.