As far as being comfortable, this one is almost a toss-up. Crowded buses and airplanes can make travel miserable, and I have experienced both sides. All things being equal, I would probably take the airplane, assuming you have no fear of flying. However, many things can play into the decision.
Flying first-class would almost always be preferable to riding in a standard, commercial bus. Of course, if the bus is a private or custom coach with large seats and plenty of room, then perhaps the bus would get my vote. I have flown to Europe several times on flights that were about half empty, and being able to stretch out over 3-4 seats and sleep made it a very comfortable flight. Of course, flying for a long period of time crowded in between two large people would not be a great experience; the same could be said for a crowded bus. One of my worst trips ever was a bus ride with many babies crying non-stop throughout the night; but again, the same conditions could arise on a plane as well.
The answer to this question is going to be contingent on many elements, one of which being personal taste. If one possesses an overwhelming fear of either mode of transport, the other mode becomes immediately desirable. I would suggest that one element of comfort that is present in air travel is that it is over relatively quickly. For example, travelling from New York to Los Angeles by plane would be much quicker than by bus, with the former being about six hours and the latter being much more. That could represent an element of comfort in that the travel is over sooner.
I feel that travel by airplane is much more comfortable than travel by bus. The speed at which airplanes travel when compared to bus travel is most important. Even if you are on the nicest bus, being stuck in one spot for to long becomes uncomfortable. Toileting is the next item for debate. When it comes to airplane and bus toileting facilities, they rate comparably. They are both small and claustrophobic. Seating on both airplanes and buses are comparable as well. Although their quality has decline, airline stewards are a definte plus. It is nice to be waited on and feel as though someone is taking care of you.
Of course, this depends a great deal on the quality of the bus. I have traveled long distances in school busses, in Greyhound busses, and in fancier, chartered busses. Of those, only the fancy busses are nicer than airplanes.
If we are just talking about the comfort once you are on the bus or plane, I think fancy busses are better, but other than that, airplanes are. To me, the major thing that matters is the quality and size of the seat. In nice busses, there are bigger seats with nicer padding than you get on an airplane.