Are you looking for a PhD program, or undergrad program?
Even in universities without structured nanotechnology programs you can participate in research groups that DO nanotech research in various departments (chem/physics/engineering, etc.) "Nanotech" is just a buzz word -- lots of places do it without directly advertising... "Optics" and "Materials Centers" etc. are often similar buzz-wordy things... only by looking at programs can you determine if the buzz-word is appropriately showing a strengthn of the institution or just being used to draw people into the institution.
So (here I'm assuming you are an undergrad)...You might think about what you want to do AFTER undergrad... do you want to go to grad school, or into industry? If you want to go to grad school, you might think about that field and be sure that as an undergrad you take coursework suitable to prepare you for the grad program... and not just be drawn by the buzz word. If, on the other hand, you want to directly enter the workforce after undergrad, getting a certificate (and more importantly EXPERIENCE) in a field is important... places with programs for undergrads are then perhaps more meaningful because they have established routes that supposedly give you the experience in the field. BUT: Look at what those routes are... places that line up internships and have SPECIAL classes (with lab components) are certainly of higher quality than those with only a "seminar" series attendance requirement or a requirement to take classes outside your major (which you could do at any institution).
If you are looking at grad -- think about your undergrad experience and how that prepared you for the given program... and really look at the faculty in the program that you would be likely be doing your research under and how much they publish, how much their work is referenced, etc...