Well the big boat called Rivet City can be there. If it was there before the bombs fell it may stayed there. ^_^
And I have no problem with the Mirelurks and the Yao Guai
Those are my thoughts too, as to how an aircraft carrier could have gotten to where Rivet City is, maybe there were some projects made to widen the river, we have no indication as to what the Potomac looks like at the present time in Fallout 3, quite possibly, some projects were made to expand it, which allowed the carrier which is now Rivet City to reach its present location.
As to mirelurks, it's already explained that they are descendant from the crabs in the area, at least that's what the player character can say when reporting about them after helping Moira research them, to me though they look most like horseshoe crabs than anothing, at least the normal ones and hunters. The mirelurk kings don't look much like other mirelurks at all, they don't even seem to have the same color of blood, and when dismembered, the broken parts of their limbs look the same as on other red blooded creatures, which makes me have to wonder if they ARE in fact mirelurks and not a different creature that people mistake for a type of mirelurk due to their tendency to frequent places where mirelurks are found. Either way though, they don't bother me at all, Fallout has lots of crazy mutated creatures anyway, adding a few more won't hurt, neither do Yao-Gui bother me, it's pretty clear what they are, and given that the player can find a number of signs of a Chinese presence in D.C., it isn't hard to guess where their name comes from.