Two options, single color LED or RGB LED.
Single Color LED: For the single color LED you would use a 6mm threaded Hollow Joystick Shaft and a Seimitsu LB-39 Bubble Balltop. The reason you'd want to use an LB-39 Bubble Balltop is that the bubbles give the LED light something to diffuse off of. Without the bubbles a translucent balltop wouldn't light up very well. You'll also need to drill the bottom of the balltop so the LED can shine through. We can do this at Paradise for you if you request it on your order sheet in the customer notes.
https://paradisearcadeshop.com/647-seimitsu-lb-39
https://paradisearcadeshop.com/371-joystick-leds
RGB LED: For the RGB LED you'd want to use a 10mm threaded JLF Hollow Shaft and a Hoku Balltop. The reason for this is that the 5mm RGB LED is too large to fit inside the 6mm threading on an LB-39 balltop. This is why you use the 10mm threading with the Hoku Balltop which also uses 10mm threading. The installation when using these is quite easy. Some customers have had success using a dremmel on their 5mm RGB LED and making it slightly smaller so it can fit into 6mm threaded hollow shaft/ LB-39 Balltop with 6mm threading. This is definitely an option, but it isn't easy.
https://paradisearcadeshop.com/paradise-arcade/560-hoku-38mm-ball-tops.html
https://paradisearcadeshop.com/hollow-shafts/1789-jlf-10mm-hollow-316l-shaft-standard.html
https://paradisearcadeshop.com/paradise-arcade-exclusive-products/556-rgb-5mm-led.html