I receive a yearly bonus and raise every December. I plan on potentially leaving my current position very early 2016 (within a couple weeks of receiving the bonus). How will it negatively affect me to put in my 2 weeks the same week I receive that bonus/raise? I currently have a great professional/personal relation with my boss and colleagues, and don't know how timing would affect recommendations/references for future positions.
That's actually pretty normal behavior and I haven't seen anyone take issue with this. It's not unusual to see a little spike in attrition after a pay out date.
There are certain types of compensation that are tied to certain conditions like performance and stay at the company: Bonus, Retention, Sign-on, stock options, stock grants, etc. All of those come with a set of rules that are spelled out in a policy or contract. As long as you play by the rule, you are doing okay and it's unlikely that anyone would consider this as "taking advantage".
Your bonus typically has an eligibility date, i.e. you are entitled to a full bonus if you are an employee in good standing (means "hasn't resigned yet") by, for example, 1/1/2016. If you resign before the date, you lose it all. If you resign after this date, you get it all. If the bonus is significant, it's perfectly rational to stay an extra few weeks unless there some specific other reason. Who wouldn't?
The companies do this intentionally. The "lose it all" rule isn't particularly fair to start with. If the company doesn't want people to leave after pay out date, they could adjust the rule so that you are always entitled to a bonus that's pro-rated to time served.
Don't just receive the bonus. Cash it before you turn in your notice just to safe. It is not about your boss. It just takes one person to abuse it. I have heard of it happening.
If you have a good relationship with your boss I don't see how waiting for bonus to pay out would be harmful. The bonus is based on what you have done - it is not a prepayment. If you resigned on Dec 1 your boss would probably wonder why you did not wait for the bonus. The bonus does not come out of your boss's check.
Because you will be putting in your two week notice the day after verifying that the bonus has been deposited in the bank you are probably fine. You will have to make sure that there isn't some other requirement such as staying a certain amount of time after the bonus is received.
You should not be putting in notice until the written offer from the new company has been signed and returned. Therefore they won't be in a position to give you a bad reference to the new employer.
Many companies as a matter of policy don't give references beyond confirming dates of employment, which in your case is perfect. If they tell employees that the company does employment verification through a third party that is a sign that they only give basic info when potential employers call for a reference.
The raise is a non-issue because the higher rate of pay stops on your last day of work.
How will it negatively affect me to put in my 2 weeks the same week I receive that bonus/raise?
If you can see the correlation of timing, so can others. No one can fully answer you how it will or will not negatively affect you, but there is no doubt timing your leaving in lieu of bonus and raise can generate red flags and suspicions.
I currently have a great professional/personal relation with my boss and colleagues, and don't know how timing would affect recommendations/references for future positions.
Your best bet if you can influence the timing factor is to set your last day beyond two weeks after a raise and bonus. Better not to raise suspicions and ruin goodwill just over a raise and year end bonus. The good will, connections and contacts are worth more than a year end bonus and raise.