Because they don’t bother the Empire
The Emperor primarily cared for crime insofar as it interfered with his sinister machinations:
“Lest any of your current activities infringe on the Emperor’s
designs,” Vader continued, “you may wish to consider relocating your
operations to sectors in the Outer Rim. Or you may opt to remain on
Coruscant and risk lengthy sentences in an Imperial prison.” He paused
to let his words sink in; then, with his gloved hands akimbo and his
black floor-length cape thrown behind his shoulders, he added: “Or
worse.”
Tarkin
Vader may have been more concerned with order, but as long as organized crime was, well, organized, and did not interfere with the proper running of the Empire, he had little quarrel with it.
Because they can be of use
The Empire in general, and indeed Darth Vader in particular, was not averse to making deals with criminal entities. For example, the Crymorah syndicate was given a certain latitude by the Empire:
“Well, clearly his heart wasn’t in it,” Tarkin said. “Strange, though,
that the Crymorah crime syndicate had no representation in your
audience.”
Vader looked down at him—blankly? Perturbed?
“We have reached an accommodation with the Crymorah,” Vader said.
Tarkin
In exchange, they provided the Empire with information on dissidents and malcontents, many of whom they could presumably observe more effectively than the Empire:
“Not entirely, my lord. The increased activities Vice Admiral Rancit
alludes to could be the result of holovids transmitted from the
Carrion Spike. COMPNOR surveillance and investigation operatives in
several sectors have noted an increase in both anti-Imperial
propaganda and mobilization among malcontent groups. ISB is making
arrests and interrogating prisoners in various Imperial facilities in
an effort to learn the identity of the culprits. As odd as it sounds,
my lord, we have also been receiving intelligence from the Crymorah
syndicate, which apparently shared some nefarious affiliation with the
criminal subcontractors who operated Phindar’s fueling station.”
Tarkin
But most important, because they don’t intend to let them remain in power
In Darth Vader #1, we see that Palpatine’s ultimate goal is to take direct control of the Outer Rim, which is where most of the criminal organizations have their operations:

So Palpatine was certainly willing to allow criminal organizations to operate while he consolidated his power. They served a useful purpose, managing resources and intelligence fairly efficiently, and generally didn’t bother his plans for worlds closer to the Core, where he was still facing fairly heavy resistance. Presumably subjugating them would have been a great deal of effort for comparatively little gain, and might even have led to short-term losses (such as the Hutts’ efficient networks of resource and information transfer). But as with the Imperial Senate, tolerating the Hutts (and any other criminal group), was merely an interim measure while Palpatine further consolidated his power. His ultimate goal, whether through the Death Star or through the Force, was ultimate personal power over the galaxy:
In the intervening years he had actually come to appreciate Plagueis
for the planner and prophet he had been. Such perilous machinations
required two Sith, one to serve as bait for the dark side, the other
to be the vessel. Success would grant them the power to harness the
full powers of the dark side, and allow them to rule for ten thousand
years.
Tarkin
So the Hutts were allowed to remain…for the time being.