When I flew a multi-destination itinerary last month (PHX-MSY / 2 days / MSY-EWR / 4 days / EWR-PHX) I had a line indicating the baggage allowance/fees for each of the legs.

OP states there was a 48-hour gap between arrival in EWR and departure from LGA. That means this is also a multi-destination trip and the baggage allowance for this final "leg" should be based on UA's policies regardless of what airline partner originated the preceding "leg". As others have said before, this is a glitch.