Originally intended to be the same size
The official marvel wiki at marvel.com has the following to say on the physical appearance of the gems.
Small oval gems approximately one inch in length; each one has a specific color: Time [Orange-Red], Space [Purple], Mind [Blue], Reality [Yellow], Power [Red-Pink], and Soul [Green].
Marvel.com - Infinity Gems
In an early appearance together on the Infinity Gauntlet, they were the same size (Infinity Gauntlet #1):
Full cover for above screenshot
Note: In their first appearance on the gauntlet (Silver Surfer Vol 3 #44) they were all the same size.
It would seem that if the gems are represented in different sizes in different issues it is up to the discretion of the author how they choose to represent them. However, Marvel seems insistent that they were each oval shaped about an inch in length and of a similar/identical size.
Due to some doubt I have found some more images showcasing their near identical size. 1, 2, 3, 4, and a whole other set of images can be found here.
The stone on the back of the hand is clearly larger than the four on the finger knuckles, the one on the thumb knuckle might be larger as well, although that is unclear.
There are 8 infinity stones, all of which are the same size, as seen by the four on the left hand glove.