Flight 11 used a Boeing
767-200ER, which has a payload of
~73000 lbs, which is enough for even a large, primitive, heavy nuclear device.
As for targets, Al-Qaeda made the right choice. The US government has significant Continuity of Government plans, with many assets located outside of DC, plus huge redundancy in the military chain of command. While a decapitation strike would be helpful in the event of military action, one bomb in the Pentagon may very well cause only a couple years' worth of staff inexperience and lost records (until the backups are found). Attack the capitol building- Congress would have been irrelevent in Martial Law (literally, rule by the military) anyway. Attack the White House, and Bush needs to get himself a few new staffers. The federal government has plans for dealing with this sort of thing, and the physical infrastructre in the city either already exists elsewhere or can be moved or rebuilt easily.
New York, meanwhile, is both a major port and has far more infrastructure (especially financial) in place. Hitting the WTC with a nuke airburst will render the entire port unusable for months at least, will require major reconstruction and has a much higher population density than Washington. NYC itself is also more compact than Washington, so more will be in the blast radius.
Economically- both the DOW and the Nasdaq stock indeces would probably be closed for weeks. The actual damage to the city could affect America's total economic output. Bonds would also stop trading, as in OTL- the largest traders are in the affected area. Martial Law would only exacerbate this.
Militarily- this is only the second time nuclear devices have been used in anger, and to a far greater death toll than the previous occasion. Afghanistan and Pakistan will probably recieve military security "aid" not only from the US, but from Russia, the PRC and Europe as well. If Bush invades Iraq, he probably will not recieve similar condemnation as he did in OTL. Prepping/survivalism will probably become far more prevalent in th eUS, with things like home canning and gun ownership becoming major things. Our national security apparatus will probably become far more extensive, possily by ATL 2020 resembling the one found in OTL PRC- indeed, preventing such an occurance is part of the reason for it in the PRC>