追加してみてください
Microsoft.EntityFrameworkCore.Tools.DotNet 1.0.0-msbuild2-final
キーはmsbuild部分ですが、それは私のために働いた。参考までに、私の.csproj全体は以下の通りです。
<Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" />
<PropertyGroup>
<OutputType>Exe</OutputType>
<TargetFramework>netcoreapp1.1</TargetFramework>
<PreserveCompilationContext>true</PreserveCompilationContext>
</PropertyGroup>
<ItemGroup>
<Compile Include="**\*.cs" Exclude="$(GlobalExclude)" />
<EmbeddedResource Include="**\*.resx" Exclude="$(GlobalExclude)" />
</ItemGroup>
<ItemGroup>
<PackageReference Include="Microsoft.NETCore.App">
<Version>1.0.1</Version>
</PackageReference>
<PackageReference Include="Microsoft.NET.Sdk.Web">
<Version>1.0.0-alpha-20161104-2-112</Version>
</PackageReference>
<PackageReference Include="Microsoft.AspNetCore.Mvc">
<Version>1.1.0</Version>
</PackageReference>
<PackageReference Include="Microsoft.AspNetCore.Diagnostics">
<Version>1.0.0</Version>
</PackageReference>
<PackageReference Include="Microsoft.AspNetCore.Server.IISIntegration">
<Version>1.0.0</Version>
</PackageReference>
<PackageReference Include="Microsoft.AspNetCore.Server.Kestrel">
<Version>1.0.1</Version>
</PackageReference>
<PackageReference Include="Microsoft.Extensions.Logging.Console">
<Version>1.0.0</Version>
</PackageReference>
<PackageReference Include="Pomelo.EntityFrameworkCore.MySql">
<Version>1.1.1-prerelease-10012</Version>
</PackageReference>
<PackageReference Include="Microsoft.EntityFrameworkCore.Tools" Version="1.0.0-msbuild2-final" />
</ItemGroup>
<ItemGroup>
<DotNetCliToolReference Include="Microsoft.EntityFrameworkCore.Tools.DotNet">
<Version>1.0.0-msbuild2-final</Version>
</DotNetCliToolReference>
</ItemGroup>
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
</Project>