CUNY schools receive their funding from New York City while SUNY schools receive funding from New York State. Other than that, and in terms of transferring to a different school within the system, the schools in each system have little to do with each other. For instance, Binghamton is an excellent school and I believe it’s the top SUNY; Stonybrook is also up there, and has particularly strong science programs. Oswego and Cortland are known “party schools”, but they are also part of the SUNY system.
Within CUNY, Queens, Hunter and Baruch are the top schools; Queens has very strong sciences, Hunter has excellent humanities, and Baruch is known for excellence in business and accounting type fields. Both Queens and Hunter also have excellent teacher education and social work programs, and I believe Brooklyn is good for that as well. As with SUNY, there are CUNY schools that do not have such excellent reputations, such as York or Queensboro (not to be confused with Queens). The top CUNY schools are as good as the top SUNY schools; and the worst SUNYs are as bad as the worst CUNYs, so state vs city makes no difference.
For both systems, you have to look into each individual school, and within each school, look into the department, as each of these schools has certain departments in which they excel more than others.
Other thing to keep in mind (at least if money is a factor for you)is that the CUNY schools are less than half the price of the SUNY schools. Either way, the most important thing is to do your research and go for the program that will best suit your needs.