Well, not really. I just looked at tomorrow's schedule. From LGA you have AA (17x), UA (18x), DL (12x) and WN (5x). UA has 34% of daily departures, but probably more in terms of actual seats since DL uses E75s.

From EWR you have AA (7x), UA/CO (8x/7x) and WN (6x). UACO has 53% of daily departures.

It doesn't seem the difference in market share (admittedly a crude analysis) is so dramatically different to cause EWR-CHI fares to be that much higher than from LGA. Especially since WN serves both. Maybe it's really DL behaving "irrationally" on this route with their shuttle service.