Are you looking for the specific command to start/stop NTP on Linux and Windows? Those are different on different Linux distros. It will be something like "/etc/init.d/ntpd stop" on some, different on others, and I'm not sure on Windows.
There are two ways to do this, and one caveat.
Method 1: Run NTP normally but stop it for the benchmark.
Method 2: Don't run NTP but run NTP in "one-shot" mode right before the benchmark runs.
(On linux that would be "ntpdate SERVERNAME" on Unix/Linux or [i think] "ntp -q" on windows)
Method 1 has some advantages in that the clock will be correct all those times that the you aren't running benchmarks. The clock will also be more accurately set for the benchmark. That is, NTP maintains the clock very accurately even between NTP packets. The NTP packets on the network are simply fine tuning. Between packets NTP uses past experience to nudge the system clock faster or slower. The disadvantage is that when you start NTP again, it will refuse to start if the clock is too far off. This is not a bug, it does this on purpose to prevent syncing to a server that has gone bad. To prevent this, do an "ntpdate" or "ntp -q" right before you restart NTP.
Method 2 has the advantage that it is more simple to implement. However, the clock will not be very accurate. "one shot" mode doesn't set the clock as accurately as running NTP. It is mostly for fixing a far-off clock before you start NTP (see above). However, if your benchmark only has to be accurate to about 1/10th second you'll be fine.
The caveat is that the benchmarks might not be benchmarking what you think they are benchmarking if you turn off NTP. The computer's clock will drift without NTP running constantly. That's ok if you are benchmarking how much drift the computer has but not much else.
(And I should note... the drift will be different not just brand-to-brand, but between particular machines.)