EntityFramework.IndexingExtensions
                                
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                        Indexing Extensions for EF6
EntityFramework.IndexingExtensions  
Indexing Extensions for Entity Framework 6
Installation
PM> Install-Package EntityFramework.IndexingExtensions
Usage
public class MyDataContext : DbContext
{
  protected override void OnModelCreating(DbModelBuilder modelBuilder)
  {
    modelBuilder.Entity<Customer>()
        .HasIndex("IX_Customers_Name",          // Provide the index name.
            e => e.Property(x => x.LastName),   // Specify at least one column.
            e => e.Property(x => x.FirstName))  // Multiple columns as desired.
        .HasIndex("IX_Customers_EmailAddress",  // Supports fluent chaining for more indexes.
            IndexOptions.Unique,                // Supports flags for unique and clustered.
            e => e.Property(x => x.EmailAddress)); 
  }
}
Notes
After publishing this, I was informed that there is an active pull request here to add something similar directly into Entity Framework. If/when that is merged, you should probably use it instead. Though, this one should continue to work without issue.