Quickly, IMHO, the issue is larger than whether or not some coherent "Israel Lobby" dictates U.S. foreign policy in the Middle East. As far as I'm concerned, M&W's merit is to hint at this larger issue, namely the discrepancy between the strategic interest of the U.S. capitalist class and the overall design of U.S. foreign policy -- overall, not only in the Middle East.
Finkelstein's article is well informed, but it assumes constant things that are not constant, e.g. that "Israel is [and, by insinuation, will be] the only stable and secure base for projecting U.S. power in this region," that "Israel [is] a unique and irreplaceable American asset in the Middle East," that "both U.S. and Israeli elites have always believed that the Arabs need to be kept subordinate," etc. When one thinks the international strategy of U.S. capitalism afresh (and big disasters lead the rulers to interrogate themselves in depth), those things are not givens -- they are endogenous variables.
Again, I recommend Peter Beinart's article in the NYT Magazine. It doesn't mention the Israel Lobby even once, yet the implications of a shift of the kind he proposes in foreign policy would be huge for the Middle East. One merit in Beinart's article, besides its clarity, is that it provides historical context -- the kind of foreign policy that now appears unthinkable was (partially at least) *the* U.S. foreign policy in the immediate postwar (e.g., vis a vis a devastated Europe) -- that is, when the U.S. was at the peak of its power in the world stage. I'm not endorsing Beinart's views. I think of his as an effort to articulate a better, lasting, more workable, more stable approach for U.S. capitalism to retain its international hegemony.
A final thought -- one schematic (but useful) way to think of the current international dilemma for U.S. capitalists is by analogy with the formation of the nation state in medieval Europe.
Julio