Yes. It's not the fastest way to do it but it can work. I would lay the tank on its side and put a paper towel on the spots then just pour vinegar on so that it's wet and let it sit for a while. If it needs to stay on a long time you can put plastic wrap over the towel to keep it from evaporating as much.
If you have to do it with the tank in its normal position (spots on a vertical surface) you could try holding the towel in place with magnets. Just be careful, don't want to break the glass with magnets.