Shopify:
- Paid installation
- Quick to set up
- Hosting included
- SSL certificate included
- Smaller theme selection
- Limited product variations
- Limited customization
- Has its own payment gateway
WooCommerce:
- Free installation
- Open source
- Unlimited customization
- Can incorporate other WordPress plug-ins
- Can use your current WordPress theme
- Search engine optimized
- Unlimited product variations
- Supports many payment gateways