Although uber does probably deserve some of the blame the mayor's attempted response was ham-fisted and bound the fail. The answer is a congestion fee like Bloomberg wanted to put in. Also eliminating most city employee parking permits and upping the cost of on-street parking to prevent circling.
As for the subway, it depends on the line. The Lexington Avenue line is the most overcrowded. More trains can't be added at this point -- at least not without CBTC (which they should really prioritize more!) The second avenue subway should help there, but that's not exactly around the corner either. After the Lexington Line the next most congested is the L, which is only relevant to a small part of Manhattan (but has big implications for growth in northern Brooklyn) and the E/F coming in from Queens until it hits midtown. That leaves the majority of Manhattan with spare subway capacity to move people around.
Specifically with respect to the East Village, it is because of crowding on the Lexington line that I suggested densification should start at the south-west part of the neighborhood which has access to the sixth avenue line subways.