3 grand. Wow, that's some budget. I have assembled a system for you. Total price of ruffly 1500 bucks.
Here is a link to the list:
Intel Core i5-6600K, Asus GeForce GTX 980, NZXT H440 (Black/Red) - System Build - PCPartPicker
Note that this is just an idea. What people value in computer hardware can be quite different. If i were to build a computer right now, this would be it.
CPU:
It had to a CPU with the latest architecture from Intel. Why Intel? Because AMD are currently quite behind in terms of architecture design.
You will find some AMD fans who will say otherwise, but most enthusiasts will agree that Intel is the way to go these days.
The latest Intel architecture is called skylake. It doesn't add much to the previous and great design called Haswell, but still enough to justify the quite small price difference. I choose the I5 instead of the I7 because the I7 is more expensive and meant as a CPU for enthusiasts and professionals. It adds nothing in terms of gaming.
Cooler:
The i5-6600K doesn't come with a cooler... not that you would want to use the stock cooler on such a CPU anyway... so i have chosen a very popular cooler. The 212 Evo. It's not the greatest but for it's price, it can't be beaten. It's good performing and keeps the noise lower than most other coolers.
If you want to go lequid cooling, i'll suggest something like Corsair H55 or H60.
Motherboard:
Has anything you need in a motherboard. Including overclocking capabilities. The only thing i can see missing is M.2 sata. If that's a problem, let me know.
It's also priced pretty good.
RAM:
I choose 8 gigabyte, because that's still plenty for most people. It had to be a 2x4 kit. It enables dual channel and gives you an extra boost in performance.
It has 2,4 ghz on the memory clock (which is at the better end of average) and a Cas Latency at 14. DDR4 memory's latency usually goes between 13 and 16. So 14 is a good number.
GPU:
This is a little difficult, I don't know if your son is eventually gonna play new tripe A titles. You should talk to him about it. But your budget is so high that i have no problem recommending a GTX 980. It's simply a great GPU. It's WAY!! overkill for minecraft. But if you want the system to be capable of upcoming triple A games in great details, i'll recommend ether this or something like the 970 or r9 290x.
I choose the Asus Strix version (same goes if you choose the 970). It should be the most quite of the bunch, but also have great cooling performance. As a bonus it has a back plate. Giving the card a more solid build.... and looks cool.
If you son never plays anything else than minecraft or similar performance required, than this is simply overkill and a waste of money. Let me know what you think.
The 980 is about $510, the 970 is about $320 and the R9-290X is about $340. The card chosen in the list is the 980.
You can check out the performance difference on all 3 here:
http://www.anandtech.com/show/8568/the-geforce-gtx-970-review-feat-evga/7
PSU:
Had to be a modular PSU and had to be at minimum gold validated. Given your budget i choose this one. I have it's little brother myself. It's amazing.
It has superb quality, nice sleeved cables and It's platinum validated (so it's very efficient)
It's made by seasonic (even though the brand is Corsair) which have a track record of delivering quality that have been recognized in the community.
It has a feature called ZeroFan. That means that it's fan only kicks in a 50% watt usages, So the fans only start spinning when he is gaming. And even when it does spin, it's very quite. So it's a quite PSU.
SSD:
The 850 Evo is a fast and reliable SSD. it's one of the most popular SATA based SSD's right now. I have it's predecessor (the 840 evo).
I choose this SSD as the only storage device in the system. That's why it had to be a big drive. 500 GB is more than the average SSD. I have officially said goodbye to mechanical drives. I don't like them. They are slow and noisy. Once you go SSD, you can't go back. Many people have a HDD as a secondary storage drives for all the big files. But since music, photos and movies are streamed instead of having them physical, i see less reason for a huge 1-3TB storage drives. I'll rather have a network harddrive away from my system that all the computers in the house can access in stead of having a noise slow HDD in my killer gaming rig. Just my 2 cents.
Feel free to add an HDD if you like.
Case.
This is a very personal opinion. I added the one i have myself to add to the total price. I can highly recommend this case.
It's good looking, quite roomy for it's size, have good cable management, a separate room for the PSU to add to it's design and hide cable mess and it also have inbuilt sound dampening material.
However the airflow isn't the best and it doesn't support DVD drives. (witch i actually like. It gives it a more slim profile because it doesn't have to make room for 5.25 inch bays)
You can find it in different color combinations. You can see it in more details here:
https://www.nzxt.com/product/detail/143-h440-performance-mid-tower.html
You can also find it in green. It's "made" by Razer (not really). So you won't find it on that website.