I don't think you want to store your ESRI Shapefiles in MongoDB. There are only two ways to store your data in MongoDB so that you might operate over them using the provided geospatial indices and queries: as GeoJSON Point, Line, or Polygon features, or as "legacy coordinate pairs." You probably want to store the same geographic features as a GeoJSON document. You can easily convert your Shapefiles to GeoJSON using GDAL's ogr2ogr:
ogr2ogr -f "GeoJSON" output_features.json input_features.shp
Next, you'll need to use MongoDB's API to insert these documents into a collection. There's a great number of client libraries to choose from for this purpose. Document insertion using any one of these APIs is very straightforward; here's an example from the Python API documentation.