It depends on which word's connotation best fits the speaker's tone of story that the phrase is in. Use either, but be aware that they are both trite expressions. Think of a surprising [like thunder] way of saying it. How about a shock of thunder, or a grab of thunder? Or punch, fit, stun, ...
And you should consider what the phrase is actually describing - some thunder is very much like a low rumbling roar while other thunder is like a the abrupt boom of a cannon going off just overhead. ___ A clap of thunder is one single bang, a roar is longer. A grab of thunder is, with respect, a no-no. It is neither trite nor creative ... However, roar of thunder always calls to mind the comically trite German nationalist song 'The Watch on the Rhine' which begins (in English translation): A mighty [or mighteous] roar ascends like thunder! It is pure kitsch.