Both can be used at any time, but "how much longer" implies that the activity is already in progress.
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We say 'gonna', but we write 'going to'.
How much longer is this going to take? This sounds like it has already taken a long time.
How long is this going to take? This does not sound like it has already taken a long time.
Clive
How long is this going to take is asking for the length of time for the entire project. How much longer is asking for the remainder from the time of the question (or answer).
long vs. longer is really the base of this question. The real question might be "was it too long" or was "it not long enough"