Either one is correct. The only difference is the focus in the sentence. "I am traveling by bus" specifies how you are going somewhere. You are going by the bus, not by car, train or airplane. "I am traveling in a bus" is perhaps less likely to be used, but if you needed to talk about your exact current location, you could say this. If you are on the phone with someone, you might say "I'm in a bus now, so it's a little noisy."

If you need to say that you TRAVEL somewhere the preposition it always "BY". e.g. I am travelling to Deli by train/ by car. If you need to say WHERE you are, then use "IN" or "ON" (some people prefer on to in :)) eg.I am in the bus. I am in the train. Hope it helps :)