TL;DR: There is good reason to believe that he wore pants, and no reason to believe that he didn't.
I searched all three books for relevant terms (e.g., pants, breeches, chaps, hose, leg, legging, knee, hip, waist, boot, sock, stocking, trousers, belt, pocket, pouch, leather, wool, linen, cloth, clout, etc), and picked out the ones that refer to Aragorn.
Fellowship of the Ring:
Suddenly Frodo noticed that a strange-looking weather- beaten man, sitting in the shadows near the wall, was also listening intently to the hobbit-talk. He had a tall tankard in front of him, and was smoking a long-stemmed pipe curiously carved. His legs were stretched out before him, showing high boots of supple leather that fitted him well, but had seen much wear and were now caked with mud. A travel-stained cloak of heavy dark-green cloth was drawn close about him, and in spite of the heat of the room he wore a hood that overshadowed his face; but the gleam of his eyes could be seen as he watched the hobbits.
High boots on a man generally accompany pants
The ground now became damp, and in places boggy and here and there they came upon pools, and wide stretches of reeds and rushes filled with the warbling of little hidden birds. They had to pick their way carefully to keep both dry-footed and on their proper course. At first they made fair progress, but as they went on, their passage became slower and more dangerous. The marshes were bewildering and treacherous, and there was no permanent trail even for Rangers to find through their shifting quagmires. The flies began to torment them, and the air was full of clouds of tiny midges that crept up their sleeves and breeches and into their hair.
Presumably, Aragorn's breeches are included
He [Aragorn] sat down on the ground, and taking the dagger-hilt laid it on his knees, and he sang over it a slow song in a strange tongue. Then setting it aside, he turned to Frodo and in a soft tone spoke words the others could not catch. From the pouch at his belt he drew out the long leaves of a plant.
Usually, belts accompany pants
Aragorn had Anduril, but no other weapon, and he went forth clad only in rusty green and brown, as a Ranger in the wilderness.
He has only one weapon - a broken and mostly useless sword - so the belt is probably for holding his pants up
With that he sprang forth nimbly, and then Frodo noticed as if for the first time, though he had long known it, that the Elf had no boots, but wore only light shoes, as he always did, and his feet made little imprint in the snow.
Frodo finds Legolas' meager footwear remarkable - wouldn't he comment on Aragorn not wearing pants?
They were so deep in the doings of the Four Farthings that they did not notice the arrival of a man clad in dark green cloth. For many minutes he stood looking down at them with a smile.
His pants are presumably dark green
Elrond was there, and several others were seated in silence about him. Frodo saw Glorfindel and Glóin; and in a corner alone Strider was sitting, clad in his old travel-worn clothes again.
Pants are an important part of "clothes"
The first part of their journey was hard and dreary, and Frodo remembered little of it, save the wind. For many sunless days an icy blast came from the Mountains in the east, and no garment seemed able to keep out its searching fingers. Though the Company was well clad, they seldom felt warm, either moving or at rest.
Well clad people usually have pants on.
The Two Towers:
Slowly Aragorn unbuckled his belt and himself set his sword upright against the wall. ‘Here I set it,’ he said; ‘but I command you not to touch it, nor to permit any other to lay hand on it. In this Elvish sheath dwells the Blade that was Broken and has been made again. Telchar first wrought it in the deeps of time. Death shall come to any man that draws Elendil’s sword save Elendil’s heir.’
Again, a belt is usually paired with pants, but now the sword is fixed, so it is probably just a sword belt
‘Here are some treasures that you let fall,’ said Aragorn. ‘You will be glad to have them back.’ He loosened his belt from under his cloak, and took from it the two sheathed knives.
This sounds like a separate, pants-holding-up belt
‘Now let us take our ease here for a little!’ said Aragorn. ‘We will sit on the edge of ruin and talk, as Gandalf says, while he is busy elsewhere. I feel a weariness such as I have seldom felt before.’ He wrapped his grey cloak about him, hiding his mail-shirt, and stretched out his long legs. Then he lay back and sent from his lips a thin stream of smoke.
Mail shirt sans pants would be uncomfortable
For many hours they rode on through the meads and river- lands. Often the grass was so high that it reached above the knees of the riders, and their steeds seemed to be swimming in a grey-green sea.
His knees would be cut to ribbons without pants here