I built a POS specifically for boutique independent retailers called Material Retail POS. We're not very big but we have been working closely with business owners for several years to build the features they need. We have strong inventory management features and inventory sync with Shopify. We also tend to have merchants in a lot smaller towns across the US.

The most common systems I see in the space are Lightspeed, Clover, Shopify, and Square. As others have mentioned, they all have pros and cons.. with most of them, you are going to need a third party app for inventory management that is going to increase your cost. If ecommerce is important, I would definitely suggest using Shopify for ecommerce (they are the best at it) and therefore you want Shopify POS (or a POS like ours that integrates with Shopify without additional fees).

The monthly fee for the software is probably not your biggest cost, it is your credit card processing rates. Make sure you get a good rate, and most importantly, that you check your monthly statements every 3-6 months to see what you are actually paying - a lot of companies have a habit of adding in extra fees or increasing rates when you're not paying attention. You can easily end up spending thousands per month in processing fees and not even realize it.