These are TLD (Top-Level Domain) extensions. .com is the most popular and universal TLD extension, whereas .in is a country specific TLD extension for India. The difference is only for segregation of businesses/websites based on their type, geographical location, etc. For example, a good quality site with .in TLD extension is more likely to come up in SERPs for a topic similar to its .com counterpart, with searches related to India or when searched in India.
If you target business from global then use with .com, another region wise target business like .in, .au, .uk...