As the first post outlined, the three options were invasion, negotiation, or a limited attack on the missile sites themselves as opposed to an all out invasion.
The problems arose because the missiles were obviously being supplied by the Soviet Union so the conflict would likely not be limited to just the US and the Cuban army/air force but would very likely expand to include other elements of the Soviet Union, something that Kennedy wanted very much to avoid. This led to the first and last options basically being off the table.
The negotiations were also tricky thanks to the fact that it wasn't as simple as picking up the phone and discussing the options but deals had to be made through back channels, etc. Eventually Kennedy agreed to give up certain US missile bases in order for the Soviets to remove their missiles from Cuba.
- First invade Cuba - unattractive though, the population would have resisted strongly
- Second negotiate a deal with USSR/Cuba which is what really happened - after a lot of posturing
- Bomb the place with out invasion but this would probably have started a new world war