I agree with Skylink on the complexity of your question. Alaska, United, and Southwest are the three big carriers along the west coast. Each one has very different programs and route structures.

Alaska has started some cross-country routes but so far only via Seattle. But they partner with CO, NW, AA, and several intl partners, giving you lots of options to price-shop and compare itineraries. You could continue your LAX-EWR flights and put the miles into an AS account (or your old CO account until you reach a redemption level). I agree with the point that its very hard to redeem via CO.

UA partners with US, DL (for the moment), and the *Alliance. I would check if one of them has a useful LAX-NYC itinerary for you. Southwest keeps to itself and doesn't venture outside US borders. For me, the lack of a international partner is a problem.

Plus, you should look at the various Visa/MC programs. Frankly, it takes some homework. Welcome to Flyer Talk!