RE: Best way to connect to CRM Online (WebAPI - OrganizationService)
Yohan,
According to me, Web API is the best way for integration, if you want to integrate with Mobile or other website. But for integration system, it depends on many factors.
You can use SSIS to integrate if you want to integrate with Database level.
You can use custom your wcf service (I recommend to use Xrm.Sdk.toolingconnector) to do that or you can use IServicemanagement to implement your integration service, you can define the class to manage the token. There is 1 sample in sample code of SDK folder.But if you choose this solution, you should consider for CRM Online, because there are limitation of plugin in crm online to connect with external service.
As I know Organization Data Service is support for CRM 2016 but maybe it will be removed in the future, hence, Web API (Odata v4) is the best way for client script to integrate system now.
Regards,