It really depends on the publication. Some online versions of print magazines are just as prestigious, while small, lesser known publications are not. As with any query, I'd include not only your best work, but the best work that relates to the query itself, print or electronic. For example, if your novel has a mystery theme and you've published mystery shorts with online markets, but your only print piece is a nonfiction on parenting, obviously the online markets match better and will feel better in the query (unless it's a parenting mystery, then you have the best of both worlds). Best wishes!