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It sounds like AWS Transfer Family is the right choice for your use case. Transfer Family is a managed file transfer service with several supported front ends (SFTP, FTPS, FTP, AS2) and backends (S3, EFS) for storage. It sounds like you have Direct Connect from an on-premises network to a set of VPCs. You can set up Transfer Family as a managed SFTP service that is only accessible within your VPC. As long as your on-premises network can resolve the Transfer Family endpoint to a private address within the VPC and has a route to that network, you can use that to upload files to S3.
An S3 VPC endpoints would provide a private, dedicated route to S3 from a VPC. It doesn't provide any managed SFTP service - you'd need to deploy and manage an SFTP server, then connect the SFTP server to S3 your self (where that connection would route over the S3 endpoint).
Thank you @bwhaley.