Yes, You can.

Either by adding --target es2015, or by adding target to Your tsconfig.json:

{
  "compilerOptions": {
    "target": "es2015"
  }
}

Supported options for target are:

• "ES3" (default)
• "ES5"
• "ES6"/"ES2015"
• "ES2016"
• "ES2017"
• "ESNext"

There are a lot of more config options. You can explore them here: Compiler options

Some options are only allowed in tsconfig.json, and not through command-line switches.

usually i use this configuration..

for typescript transpiling my tsconfig.json:

{
  "compilerOptions": {
    "outDir": "app_build/",
    "target": "es6", // <-- TARGETING ES6
    "module": "commonjs",
    "moduleResolution": "node",
    "lib": [
      "es5",
      "dom"
    ],
    "sourceMap": true,
    "emitDecoratorMetadata": true,
    "experimentalDecorators": true,
    "removeComments": false,
    "noImplicitAny": false
  },
  "compileOnSave": true,
  "exclude": [
    "node_modules",
    "app_build/js",
    "typings/main",
    "typings/main.d.ts"
  ]
}

My Webpack dev file (webpack.dev.js):

var ExtractTextPlugin = require("extract-text-webpack-plugin");
var webpack = require("webpack");
var HtmlWebpackPlugin = require("html-webpack-plugin");
var CleanWebpackPlugin = require('clean-webpack-plugin');
var path = require('path');

module.exports = {
    entry: {
        "polyfills": "./polyfills.ts",
        "vendor": "./vendor.ts",
        "app": "./app/main.ts",

    },
    resolve: {
        extensions: ['', '.ts', '.js', '.json', '.css', '.scss', '.html']
    },
    output: {
        path: "./app_build",
        filename: "js/[name]-[hash:8].bundle.js"
    },
    devtool: 'source-map',
    module: {
        loaders: [
            {
                loader: "babel-loader",

                // Skip any files outside of your project's `src` directory

                exclude: [
                  path.resolve(__dirname, "node_modules")
                ],
                // Only run `.js` and `.jsx` files through Babel
                test: /\.js/,

                // Options to configure babel with
                query: {
                    plugins: ['transform-runtime', 'babel-plugin-transform-async-to-generator'],
                    presets: ['es2015', 'stage-0'], //<-- BABEL TRANSPILE
                }
            },
            {
                test: /\.ts$/,
                loader: "ts"
            },
            {
                test: /\.html$/,
                loader: "html"
            },
            //{
            //    test: /\.(png|jpg|gif|ico|woff|woff2|ttf|svg|eot)$/,
            //    loader: "file?name=assets/[name]-[hash:6].[ext]",
            //},
            {
                test: /\.(png|jpg|gif|ico)$/,
                //include:  path.resolve(__dirname, "assets/img"),
                loader: 'file?name=/assets/img/[name]-[hash:6].[ext]'
            },
            {
                test: /\.(woff|woff2|eot|ttf|svg)$/,
              //  exclude: /node_modules/,
                loader: 'file?name=/assets/fonts/[name].[ext]'
            },
            // Load css files which are required in vendor.ts
            {
                test: /\.css$/,
                loader: "style-loader!css-loader"
            },
            {
                test: /\.scss$/,
                loader: ExtractTextPlugin.extract('css!sass')
            },
        ]
    },
    plugins: [
        new ExtractTextPlugin("css/[name]-[hash:8].bundle.css", { allChunks: true }),
        new webpack.optimize.CommonsChunkPlugin({
            name: ["app", "vendor", "polyfills"]
        }),
        new CleanWebpackPlugin(
            [
                "./app_build/js/",
                "./app_build/css/",
                "./app_build/assets/",
                "./app_build/index.html"
            ]
        ),
        // inject in index.html
        new HtmlWebpackPlugin({
            template: "./index.html",
            inject: "body",
            //minifyJS: true,
            //minifyCSS: true,
        }),
        new webpack.ProvidePlugin({
            jQuery: 'jquery',
            $: 'jquery',
            jquery: 'jquery'
        })
    ],
    devServer: {
        //contentBase: path.resolve(__dirname, "app_build/"),
        historyApiFallback: true,
        stats: "minimal"
    }
};

I use it for an Angular 2 project .. hope it helps you