Depends on there defenses and what you are willing to do. Sub launched cruise missiles would be a good idea if they had heavy defenses and you were willing to spend time to coordinate your submarines, get them into position and launching together, and figuring out targets.
Ships might be a good idea if they don't have really heavy defenses against ships and you have a list of targets at the ready.
Planes probably works best if you don't have all of your targets planned out, and some missiles might have to be delivered spontaneously.
The reality is for a strong first strike you will probably use a combination of all of them. Subs and ships striking at the larger fixed targets, while planes target smaller moving targets. From the sounds of your set up I would probably use sub and ship launched missiles to target enemy command and control centers plus fixed air defense positions. Planes can then sweep in and target non fixed defenses, and carry out SEAD operations.
Is this all in preparation for landing troops?