I hope you understand that funding has been very tight overall, and given the recent budgetary cutbacks, funding will be exceptionally tight this year. This will effect all schools, in particular how many students are accepted. Considering the cost of tuition at both MIT and Harvard, plus their higher stipends for students (due to cost of living increase in the city), the pressure to accept fewer students will be greater than, say, a state university. Keep in mind that the total cost of a experimental phd student at, say MIT, is on the order of $500,000 (funded by grants, ie, the taxpayer, theoretical students also tend to cost less). This figure seems very high (honestly, I see no reason why it shouldn't be lower and more in line with say, state schools), but it is a decent rule of thumb.
Consequently, I hope that you either: a) currently attend either university and have a research group firmly lined up and/or b) have another option other than grad school if both options happen not to work out. Given the current state of the sciences, I hope one (or both) accept you, but I would recommend apply to at least one backup school. Best of luck![/i]