You can use Wordpress/Woocommerce + FreeScout with some addons to enhance your workflow.
Woocommerce Integration for FreeScout: https://freescout.net/module/woocommerce/
The integration lets you see billing history of your clients in a sidebar within Freescout.
WP Cost Estimation plugin:
https://codecanyon.net/item/wp-cost-estimation-payment-forms-builder/7818230
You can use this plugin to create unique forms with the ability to check out directly using Stripe, PayPal, etc..
For example, you add your "products" which in your case would be apps, # of users, etc.. and assign pricing to each option. Then, your client can self-build a package and pay for it.
This is one route. You could look into Chatwoot if you're looking to have live chat, email, and social media messages all in one dashboard.
BTW, you can set up recurring billing from within Stripe's dashboard and skip Invoice Ninja altogether. However, you get more flexibility with IN.