I have done both and had success with both. They are two very different programs. Sheiko is a lot of work and you will spend a lot of time in the gym. A complaint I hear a lot with Sheiko is that people get bored doing the three main lifts and don't like the lack of variety. 5/3/1 is easier to customize to your needs and Sheiko is several set templates.
There are no deloads with Sheiko. You have to adapt to Sheiko instead of having the program adapt to you. The accessory work is very limited with Sheiko. Sheiko is a high volume program and some people do okay with it, but for some it is too much volume. You can get strong on Sheiko. It worked great for my squat and deadlift, but didn't work so well for my bench. 5/3/1 worked great for all three lifts.
The nice thing about 5/3/1 is that I was able to adjust the volume to fit my needs on the squat, bench and deadlift. On squat I would follow up squats with front squats, on bench I would follow up with close grip bench, DB incline bench, and with the deadlift, I only deadlifted. Accessory exercises are a good way to bring up weaknesses and Sheiko doesn't allow the flexibility with accessory exercises.
5/3/1 is going to be easier to stick with. You could just adjust the frequency of your lifts with 5/3/1. You could do this by having a light squat day on a deadlift day. You could always add another day of benching. Customize it and learn how to train yourself, once you figure out what works and how to manipulate it when you need to, you will do much better.