I must start this question by saying that I have very little knowledge of javascript (I\'m practiced in Java) and just wanted to make a (somewhat) simple Discord bot that would
Your issue is, that you mix discord.js with discord.io
discord.js is object oriented where discord.io is not, so in discord.io your message is already a string!
Example discord.io message event.
bot.on('message', function(user, userID, channelID, message, event) {
    if (message === "ping") {
        bot.sendMessage({
            to: channelID,
            message: "pong"
        });
    }
});
Maybe jam something like if(!msg || !msg.content) return; in there to bail out if the msg object or its content property is undefined. 
bot.on('message', (msg) => {
  if(!msg || !msg.content) return;
  if (msg.content.startsWith(prefix + "on")) {
        if (randOn) {
            msg.channel.sendMessage("Already running.");
        }
        else {
            msg.channel.sendMessage("Random message started.")
        randomMessage = setTimeout(function() {
                randMsg(msg.channel);
            }, 1000*timer[0]);
        }
  }
  else if (msg.content.startsWith(prefix + "off")) {
        if (randOn) {
            clearTimeout(randomMessage);
            msg.channel.sendMessage("Random message disabled.");
        }
        else {
            msg.channel.sendMessage("Not running.");
        }
  }
});