Why do you have to ‘go by’ anything now that you are in a program? Do you really think that those numbers are official? or that granular? Numbering universities implies and accuracy that simply is not there. And which ranking are you talking about, there are all sorts of different rankings using differing methodologies and having differing agendas. If you are studying computer science different universities could (and are) ranked by subfield in CS. Some lower ranked can be stronger in any particular area by having a very strong research group. But yes, I suppose the CS ranking are more to the point, but there are overlaps in your area, aren’t there?
As you have found, you have to look at a combination of factors when choosing a university and funding is an important one. But also the fit in the department interest with yours, and especially who your professor is and what kind of support you get are much bigger factors that a couple of minor points among top uni’s from a magazine. Mistake? Get some perspective I say. But to make you feel better, maybe you should look at this ranking were they are only 2 apart, or 1 apart for US only.
http://www.shanghairanking.com/SubjectCS2014.html