Onions are fine, not seen them mentioned anywhere in any pregnancy warnings at all. You need to eat loads of fruit and veg or you could get piles!
I don't think you're at all likely to get listeria from things which come in their own natural wrappers (skins), wonder if that would help you eat more? Things like bananas, oranges, onions, avocados, anything where you don't eat the skin would be peeled just before you eat it, so isn't going to have had a chance to get listeria, even if you're paraniod about other veg. Do make sure you get enough fibre!
The source of listeria would be the soil the plant is grown in, so anything that gets peeled at any point after it is picked should really be very low risk. Some more I can think of are mangoes, coconuts, pomegranite, squash, marrow, peas, melons, pineapple, papaya, beetroot... plus of course you could peel things which don't usually get peeled if you felt like it! Probably easier to just wash some things though, plus there's a lot more of the fibre you need in the skins of a lot of things.