1. Rent a car and drive-The fastest, and probably leat expensive option, it also gives you a way to get around in SD and allows you to be on your own schedule.
2. Amtrak-unless you hit bad traffic driving which is a possibility but can be planned around it takes a little longer and I think is about $56 round trip per person.
Renting a car is a good option. But what do you want to see and do in San Diego? For some places like Old Town or the Midway, there are hop on hop off buses. To see beaches and Highlands you should get a car. Suggest you research a bit on your intended sights in San Diego. Personally I would spend a good chunk of the day at the world class zoo and its Balboa Park environs, but I'm not you.
IF you have a couple of extra days I'd spend them in San Diego and not just go for one day. We are a large city with lots to see/do depending on your interests.
The train is an easy way to get to San Diego . The last stop is in downtown where you can pick up the hop on hop off tour if you like. It has 2 routes. One goes to beaches and one goes to more of the city sights.
See here: www.trolleytours.com
Rent a car and drive. The train is slower and limits you.