We will be driving out of Switzerland with our rental car and visiting Cinque Terra in early September. Spending two nights in the area and walking the trail. Our problem is the rental car.

We would like to stay in Vernazza. Would it be better to stay outside of the CT area, where we could just leave the car at our hotel and take the train in for the day. Or park the car someplace so that we can spend the night.

Is there any safe, secure and inexpensive parking options?

If you want to stay in one of the 5 villages then you can either drive into Vernazza.... it will take a little time and the road is narrow but it is a beautiful drive. Or you can park your car in Lerici and take the ferry into Cinque Terre (if the seas are rough and the ferry is not running then just drive into your town).
Vernazza is our favorite village and we usually stay at Gianni Franzi. http://www.giannifranzi.it/

I believe that one can park in Monterosso-al-mare (sp?) at some of the hotels there. It is the farthest north of the five towns.

When we stayed in Vernazza 5 years ago, we had a rental car for the last two days of our visit. There is a parking lot above the town; even residents can't drive into Vernazza. There is a shuttle that runs you down to the gate into town but from there you have to carry your bags to your room. (We travel light so it was not a problem.)

I think the lot was watched and the price was reasonable.

Park in Monterosso--big lot by the beach.

We parked at the big lot at Monterroso and our hotel picked us up at the lot with a "pick-up". However, the parking fees were very high. Can't remember the exact amount and they charge for a full day even if it's for 8 hours, etc. There is some free parking in the town (if you can find a place!)