Simply put: No.
You can only shoot Mini-Nukes with the Fat Man.
Other than this: Yes.
During the The Power of the Atom quest, you have the option to save, or destroy Megaton. You can accept to do the job for Mr. Burke. Read more about it here: http://fallout.wikia.com/wiki/The_Power_of_the_Atom Sit back and enjoy the fireworks, while they last.
No other nukes are available, but you can still find certain things that can produce some explosions.
You can falsely launch a nuke at http://fallout.wikia.com/wiki/Fort_Constantine, there is an ICBM that can be "LAUNCHED", this makes the room shake, though the terminal states it failed to launch. A lot of nukes can be found in the "Bomb storage" area.
You can also launch a series of 'micro-nukes' from Satcom Array NW-05a in the northwest sector of the map (south-east of Raven Rock). Inside one of the Arrays you will find a hostile Ghoul scientist - kill her and use the passcode from her corpse on her terminal to activate the 'Highwater Trousers' orbital platform, which launches eight micro-nukes outside the Satcom Array, which you can watch from the upper gantries.
Finally, as of the Broken Steel DLC, as part of the final quest (Who Dares Wins) you have the choice of launching a nuclear attack on either the Enclave Mobile Crawler Base at Adams Air Force Base or on the Brotherhood of Steel Citadel in the D.C. ruins.
IF YOU HAVE THE PC VERSION OF FALLOUT 3 YOU CAN CHEAT FOR LIBERTY PRIME WEAP BOMBS WHICH ARE FULL SIZED NUKES!! ZYNIA