Tell now or tell later?  That's a decision that only you can make, particularly as we don't really know the set up in your company.

There are two ways of dealing with this - both of which are right and tactful in their own way depending upon the circumstances:

If you are authorized to read your boss's emails - and ONLY if you are - then you should go to him and say that you have read an email on his system that you clearly weren't meant to see, describe the contents and say how disappointed you are about the contents, it reflects badly on your performance, you thought that any problems would have been flagged up sooner etc etc.  And see where the conversation goes.  

If you are NOT authorized to see his emails, then keep schtum until your appraisal.  If that is the case, then at your appraisal you can say how sad you are that this was brought up earlier so that you had the opportunity to address any concerns that management had and work through them sooner etc etc.

Either way you come out on top - but you need to be very sure of the ground you stand on first.