While the best places offer both (Bascom, Emory, Iowa, Michigan, USC, Duke..), there are exceptions to the rule. For example, most people that end up at Mass Eye and Ear end up doing fellowships. This is likely due to the fact that most selected for training here end up going into academics. However, you want to make sure you end up at a program where you do not need a fellowship to feel comfortable for practice.
In other words, go to the best program you can - your primary focus in residency should be on clinical / surgical ophthalmology. Academic interests are important, but they should be of #2 priority.
Without a home program, you must do away electives to obtain at least 2 ophthalmology letters of recommendation. Perhaps spend some time with a local community ophthalmology clinic before you go out to do your "audition" electives. Do not use the community ophthalmologists for a LOR unless he/she is famous.