The solution is that you import hdkey from the ethereumethereumjs-wallet library. hdkey is being exported and it is not the default export.
const {hdkey} = require('ethereumjs-wallet');
const mnemonic = bip39.generateMnemonic();
const seed = bip39.mnemonicToSeedSync(mnemonic);
const hdWallet = hdkey.fromMasterSeed(seed);