I think the El switches to surface buses around 0:30, depending on exactly where you're getting on.

My only experience with taking MegaBus from New York (to Boston) was horrid; I think we wound up leaving about two hours after originally scheduled, with a similar sort of domino effect, and employees who were rude and unhelpful about the situation. Bolt seems generally more reliable, though I have found MegaBus fine between Boston and New Haven (which is a much less popular route).