this one is actually a bit confusing because VIT Pune and VU (Vishwakarma University) are essentially the same institution under different branding.
VIT Pune = Vishwakarma Institute of Technology, Pune (the original college name, an autonomous engineering college affiliated to Savitribai Phule Pune University). it recently received university status and is now referred to as Vishwakarma University in some contexts.
so if someone is comparing "VIT Pune" vs "Vishwakarma University Pune" — they're comparing the same college pre and post university status grant. they're not two separate colleges.
if you're asking about the difference after the university status:
if however you're comparing VIT Pune (Vishwakarma) with VIT Vellore's Pune campus — those are completely different institutions. VIT Vellore is a much more established and reputed college for CSE/ECE. don't confuse the two!
Although both VIT Pune and VU Pune are run by the same trust BRACT, both are completely different colleges. VU is a relatively new college whereas VIT Pune is an old college established around 1986 with a rich legacy. VIT Pune is well-known for its excellent placement record whereas CU Pune is quite lacking in this aspect. VIT Pune has a well-versed faculty with an updated curriculum. It also offers a vibrant campus life with many fests. VU Pune has a bigger campus.
In all, VIT Pune is a better choice than VU Pune.