Both are equally good cloud storage mechanisms -- here's the pros and cons of each so you can make the best decision for your projects.

Incremental improvement to Azure Mobile Services .NET Backend Azure Storage Extension and Windows Azure Mobile Services will ease table navigation pain with Web apps.

Azure Cosmos DB also plays nice with several NoSQL APIs including MongoDB, Table Storage, DocumentDB SQL, Gremlin, and Azure Tables. The Gremlin and Table Storage are currently in preview mode.